Ok this one seems to be somehow difficult if no one knows any work around this issue.
I think there is some way of rendering passes from the mib_color_mix as this is the final shader that the render reeds. The problem I think is also in the way how maya and MR are writing the alpha's, I think they use different info. for representing the alpha channels. I've seen some guys were recommending creating a custom frame buffers but not sure how to do it with the mib_color_mix.
Why they need to do something if doesn't work with the industry standards.